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- PDB-6ar3: Structure of a Thermostable Group II Intron Reverse Transcriptase... -

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Basic information

Entry
Database: PDB / ID: 6ar3
TitleStructure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications (RT/Duplex (Se-Met))
Components
  • DNA
  • GsI-IIC RT
  • RNA
KeywordsRNA binding protein/RNA/DNA / Polymerase / RNA binding protein-RNA-DNA complex
Function / homology
Function and homology information


RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / defense response to virus / RNA binding / metal ion binding
Similarity search - Function
Group II intron, maturase-specific / Group II intron reverse transcriptase/maturase / Group II intron, maturase-specific domain / RNA-directed DNA polymerase (reverse transcriptase), msDNA / : / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA-directed DNA polymerase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.41 Å
AuthorsStamos, J.L. / Lentzsch, A.M. / Lambowitz, A.M.
CitationJournal: Mol. Cell / Year: 2017
Title: Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications.
Authors: Stamos, J.L. / Lentzsch, A.M. / Lambowitz, A.M.
History
DepositionAug 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GsI-IIC RT
B: DNA
C: RNA
D: GsI-IIC RT
E: DNA
F: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,82110
Polymers115,7906
Non-polymers1,0314
Water00
1
A: GsI-IIC RT
B: DNA
C: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4105
Polymers57,8953
Non-polymers5152
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-19 kcal/mol
Surface area21790 Å2
MethodPISA
2
D: GsI-IIC RT
E: DNA
F: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4105
Polymers57,8953
Non-polymers5152
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-18 kcal/mol
Surface area21990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.527, 108.966, 72.517
Angle α, β, γ (deg.)90.000, 113.780, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAARGARGAA2 - 4182 - 418
21ALAALAARGARGDD2 - 4182 - 418
12DCDCDCDCBB1 - 111 - 11
22DCDCDCDCEE1 - 111 - 11
13UUGGCC1 - 141 - 14
23UUGGFF1 - 141 - 14

NCS ensembles :
ID
1
2
3

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Components

#1: Protein GsI-IIC RT


Mass: 50133.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: trt / Production host: Escherichia coli (E. coli) / References: UniProt: E2GM63
#2: DNA chain DNA


Mass: 3303.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA


Mass: 4457.636 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.502
11H+4/2L, -K, -L20.498
ReflectionResolution: 3.41→48.93 Å / Num. obs: 17494 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.224 / Rpim(I) all: 0.087 / Rrim(I) all: 0.24 / Net I/σ(I): 9.2 / Num. measured all: 132418 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.41-3.697.60.8535710.8840.330.91299.7
9.03-48.937.10.0399770.9990.0160.04299.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.22data extraction
XDSMay 1, 2016data reduction
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KYL, 5IRF

3kyl

5irf


Resolution: 3.41→48.93 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.84 / SU B: 34.161 / SU ML: 0.548 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : REFINED INDIVIDUALLY Twin refinement in Refmac5 with twin fraction=0.5 and twin operator=h+2*l,-k,-l.
RfactorNum. reflection% reflectionSelection details
Rfree0.3237 1736 9.9 %RANDOM
Rwork0.2732 ---
obs0.2783 15756 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 198.59 Å2 / Biso mean: 96.135 Å2 / Biso min: 32.35 Å2
Baniso -1Baniso -2Baniso -3
1--65.75 Å2-0 Å2-55.26 Å2
2--37.03 Å20 Å2
3---28.72 Å2
Refinement stepCycle: final / Resolution: 3.41→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6576 1022 62 0 7660
Biso mean--87.19 --
Num. residues----887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0187926
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.84610970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0285835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31922.258310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.557151086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8031580
X-RAY DIFFRACTIONr_chiral_restr0.0790.21209
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215748
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A261020.06
12D261020.06
21B17500.04
22E17500.04
31C25120.03
32F25120.03
LS refinement shellResolution: 3.411→3.499 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 124 -
Rwork0.325 1153 -
all-1277 -
obs--97.41 %

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